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Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars

文献类型： 外文期刊

作者： Yuan, Yang 1 ; Zhang, Qijun 3 ; Zeng, Shuiyun 2 ; Gu, Longjiang 2 ; Si, Weina 2 ; Zhang, Xiaohui 2 ; Tian, Dacheng 2 ; Ya 1 ;

作者机构： 1.Nanjing Agr Univ, Coll Agr Sci, Appl Plant Genom Lab, Nanjing 210095, Jiangsu, Peoples R China

2.Nanjing Univ, Sch Life Sci, State Key Lab Pharmaceut Biotechnol, Nanjing 210023, Jiangsu, Peoples R China

3.Jiangsu Acad Agr Sci, Nanjing 210014, Jiangsu, Peoples R China

关键词： japonica;indica;Wild rice;Domestication;Resequencing;Functional genes

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2017 年 18 卷

页码：

收录情况： SCI

摘要： Background: Asian cultivated rice (Oryza sativa L.), including japonica and indica, is unarguable the most important crop in Asia as well as worldwide. However, a decisive conclusion of its origination and domestication processes are still lacking. Nowadays, the ever-increasing high-throughput sequencing data of numerous rice samples have provided us new opportunities to get close to the answer of these questions. Results: By compiling 296 whole-genome sequenced rice cultivars and 39 diverse wild rice, two types of domesticated regions (DR-I and DR-II) with strong selective sweep signals between different groups were detected. DR-I regions included 28 blocks which significantly differentiated between japonica and indica subspecies, while DR-II regions were consisted of another 28 blocks which significantly differentiated between wild and cultivated rice, each covered 890 kb and 640 kb, respectively. In-depth analysis suggested that both DR-Is and DR-IIs could have originated from Indo-China Peninsula to southern China, and DR-IIs might be introgressed from indica to japonica. Functional bias with significant positive selection has also been detected in the genes of DR-I, suggesting important role of the selective sweep in differentiation of japonica and indica. Conclusions: This research promoted a new possible model of the origin of the cultivated rice that DR-Is in japonica and indica maybe independently originated from the divergent wild rice in the Indo-China Peninsula to southern China, and then followed by frequent introgression. Genes with significant positive selection and biased functions were also detected which could play important roles in rice domestication and differentiation processes.

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